E2M2: Ecological & Epidemiological Modeling in Madagascar

January 13-20 & January 22, 2018
Centre ValBio, Ranomafana National Park & Institut Pasteur de Madagascar, Antananarivo
Along with Tanjona Ramidantsoa, I organize E2M2: Ecological and Epidemiological Modeling in Madagascar, an annual workshop for Malagasy students aimed to provide an introduction to the use of dynamical models in understanding ecological and epidemiological data. Students participate in a series of interactive lectures and computer-based tutorials and learn to fine-tune model-based research questions, develop clear model frameworks and corresponding equations, and fit models to real-world data. All students work closely with peers and instructors to develop a research plan for an ongoing or existing project integrating dynamical modeling with data collection and/or analysis in a biological system of their choosing. These research plans can then be used as a foundation for future dissertation or grant proposals.
Our 2018 clinic will take place from January 13-20, 2018 at Centre ValBio, Ranomafana National Park, Madagascar, with a mandatory closing session to follow at Institut Pasteur de Madagascar on January 22.
Our teaching team is comprised of: Matthew Bonds, Cara Brook, Andres Garchitorena, Jessica Metcalf, Calistus Ngonghala, Tanjona Ramiadantsoa, Fidisoa Rasambainarivo, Julio Rakotonirina, Hafaliana Christian Ranaivoson, and Amy Wesolowski.
2018 Syllabus:
Please follow instructions for installing packages in R here.
Follow along with R tricks posted through the week here.
Sat, Jan 13: (Travel)
- 6:30am: Depart from Tana (Institut Pasteur) via bus, travel to Ranomafana (lunch stop Antsirabe)
- 6:30-7:30pm: Dinner
- 7:30-8:30pm: Introductions and Road Map: What are we doing here? (Cara)
Sun, Jan 14: “Thinking About Data”
Mon, Jan 15: “Deeper Thinking About Data”
- 6:30-8:00am: Breakfast
- 8:00-8:15am: Road Map and Daily Agenda (Cara)
- 8:15am-9:45am: Lecture/Tutorial: Introduction to mixed modeling (Andres)
- 9:45 - 10:00am: Coffee Break. Prep for hike!
- 10:00am-1:00pm: Morning walk in Ranomafana National Park
- 1:00pm-2:00pm: Lunch
- 2:00 - 3:00pm: Writing Exercise: Formulating research questions (HW) (Cara)
- 3:00-3:30pm: Break
- 3:30-5:00pm: Lecture/Tutorial: Introduction to occupancy modeling (Fidy)
- 5:00-6:30pm: Free time, or one-on-one mentoring
- 6:30-7:30pm: Dinner
Tues, Jan 16: “Thinking About Mechanism”
Wed, Jan 17: “Fitting Models to Data”
- 6:30-8:00am: Breakfast
- 7:00-8:00am: Mentoring as needed
- 8:00-8:30am: Road Map and Daily Agenda (Cara)
- 8:30-10:30am: Lecture/Tutorial: Model Fitting in Practice – the Basic Concept (Cara)
- 10:00-10:30am: Break
- 10:30-12:00pm: Exercise: Epidemics Cards (Cara + Amy)
- 12:00-1:00pm: Lunch
- 1:00pm-2:00pm: Tutorial: Model Fitting with Epidemic Cards (continued from above) (Amy)
- 2:00-3:30pm: Model Telephone with Model Diagrams (Mentors: Jean-Marius, Ornella, Antso)
- 3:30-4:00pm: Break
- 4:00-5:00pm: Lecture: PIVOT’s Role in E2M2 (Andres)
- 5:00-6:30pm: Mentor research presentations (Jean-Marius, Ornella, Antso)
- 6:30-7:30pm: Dinner
Thurs, Jan 18: “Refining Your Work”
Fri, Jan 19: “Putting it all in Perspective”
Sat, Jan 20: (Travel)
- 6:00-6:30am: Breakfast to go
- 6:30am: Board bus
- Return to Antananarivo
Mon, Jan 22: “Sharing Your Work” (at Institut Pasteur de Madagascar in Antananarivo)
- 9:00-11:00am: Closing ceremony and final student presentations (Cara)
- 11:00am-12:00pm: Final Feedback Session (Julio)
- 12:30-2:00pm: Farewell lunch
- 2:00-4:30pm: Mini-symposium: “Modeling Insights Into Epidemiology and Ecology” (Instructor presentations)
- Cara Brook “Malagasy fruit bats as reservoirs for emerging viral zoonoses” (20 min. + 5 min. Q/A)
- Tanjona Ramiadantsoa “Importance of large scale corridors for biodiversity conservation” (20 min. + 5 min. Q/A)
- Jessica Metcalf “Vaccine preventable diseases: mathematical modeling for public health” (20 min. + 5 min. Q/A)
- Amy Wesolowski “”Using novel data sources to understand the spatial distribution of vector-borne diseases" (20 min. + 5 min. Q/A)
- Fidy Rasambainarivo “Interactions and disease transmission at the domestic animal-wildlife interface in Betampona, Madagascar” (20 min. + 5 min. Q/A)
- 4:30pm: Social Hour
Many of the materials and methods used in E2M2 were adapted from those previously developed by faculty at ICI3D:
